April 2012 Archives

This should be of broad interest: a symposium at Stanford School of Law on the 1987 Supreme Court decision Edwards v. Aguillard. This is the decision that ruled “creation science” to be a sham devised to promote religion in the classroom. And, of course, the decision led directly to the decision to drop creationist terminology and adopt “intelligent design” terminology.

Now that Shinola is no longer manufactured, I have to wonder what Ken Ham shines his shoes with. Today, Mr. Ham, the alleged proprietor of a putative Ark Park in Kentucky, ran a piece that criticizes the Kentucky Horse Park for promoting “(outdated) evolutionary ideas.”

Of all the fatuous nonsense in that article, this claim may be the, um, best:

One popular belief in regard to the horse evolution series is that as horses supposedly evolved, they got bigger. Eohippus is listed as 14 inches tall, while Mesohippus is listed as 24 inches tall. The next two horses in the display, Miohippus and Merychippus, grow steadily bigger. What’s the problem, though, with the belief that horses somehow evolved into larger and larger animals? If that were true, shouldn’t we see only very large horses today? But we don’t–horses vary in size from the Clydesdale to the much smaller Fallabella (just 17 inches tall).

I will not bother to explain that the domesticated horses we see today are products of artificial selection. Rather, I will note that Mr. Ham’s “deduction” is equivalent to saying, “If we are getting generally taller, then why is my granddaughter shorter than her mother?” Or, if you prefer, “If IQ’s are generally increasing, then why do we still have creationists?”

Acknowledgment. Thanks to Dan Phelps for the link. I am truly impressed that Mr. Phelps has the patience to track this kind of bunk.

I’ve been rereading “Monkey Girl,” (Amazon; Barnes&Noble) Edward Humes’ excellent book on the Kitzmiller trial, and ran onto something I’d either missed first time through or forgotten. As is the case in the Freshwater affair, the Rutherford Institute got involved in Kitzmiller. It represented three sets of Dover parents who requested that they be allowed to intervene in the case, joining the school board as defendants. Filed the same week that the Board’s intelligent design-based statement was read to the first classes in school, the Application to Intervene argued that those parents had a stake in the outcome of the trial, and therefore should be allowed to participate as defendants, represented, of course, by the Rutherford Institute.

The Rutherford Institute argued on behalf of the three sets of parents that if the plaintiffs (Tammy Kitzmiller, et al.) prevailed and the ID statement to biology classes was forbidden to be read, their children would not be able to hear about intelligent design. The Application to Intervene as Defendants (PDF) claimed that

The Intervenors seek to participate in this action because, if the Plaintiffs are successful, the lawsuit will have the effect of censoring the Dover Area School District Board and shielding all ninth graders from criticism of Darwin’s Theory of Evolution.

…

[The intervenors] seek to ensure that their children will have full access to information concerning the theory of evolution, including its many gaps for which there is no evidence. The Applicants further seek to ensure
that their children not be denied access to a critical analysis of evolution merely because some persons believe that critics of the theory are religiously motivated. (pp. 2-3)

Further, in the Application to Intervene Rutherford argued that parents of school children are entitled to assert a “… First Amendment right of access to information and ideas in an academic setting…”. Still further,

The Applicants have a substantial legal interest, rooted in the First
Amendment, in making sure that their children are not prevented from learning about intelligent design.

That is, parents are constitutionally empowered to determine what should be covered in public school science curricula, regardless of whether it’s accepted science or fringe pseudoscience. Consistent with Michael Behe’s and Scott Minnich’s admissions in their Kitzmiller testimony that their redefinition of science would substantially broaden the landscape of admissible explanations in science, extending it into the supernatural, the Rutherford Institute’s argument would pave the way for the return of astrology and alchemy to the science classroom, should some parent or teacher wish it.

In a way the route for Rutherford Institute’s involvement in both Dover and Mt. Vernon was similar. Rather than being a principal actor, involved in the original disputes, Rutherford was a late-comer, entering the processes well after they were in progress. It attempted (in Dover) and succeeded (in Mt. Vernon) in inserting itself into an on-going process, making arguments that neither side made prior to Rutherford’s participation. In both cases it is arguing for an expansion of First Amendment rights, in the Dover case the right of parents to determine what will be taught in public school science classrooms, and in the Mt. Vernon case the right of a teacher to override instructions from the Board of Education regarding curriculum matters. And in both cases the result would be the inclusion of any damn fool thing a parent or teacher wants taught, regardless of its appropriateness to the class or the validity of its content. As the response from the plaintiffs in opposition to the Application to Intervene put it,

Second, if Applicants were correct that there is a First Amendment right of parents to dictate the content of public school curricula, that right would eviscerate the well-recognized authority of school districts to set their own curricula. (p. 7)

The Rutherford Institute’s argument has developed and been elaborated in the seven years between Kitzmiller and Freshwater, but it rests on the same foundation: A claimed First Amendment right to allow anything at all to be taught in science classes, subject only to the idiosyncratic wishes of individual parents or teachers.

1. Coyne’s attempt to blame religion-in-general for creationism (instead of, say, fundamentalism) using correlations between economics, religion, and creationism, misses a huge and obvious alternative hypothesis, which is that the real explanatory variable in changing minds to accept evolution is level of education.

One of the salient properties of anti-evolutionist coverage of the Freshwater affair has been a systematic misrepresentation of the case. On various anti-evolutionist blogs and Christian news outlets, the case has consistently been characterized as being concerned solely with Freshwater’s personal Bible on his desk, excluding any mention of the various religious items displayed in his classroom, his use of blatantly creationist materials in class, his insubordination, and his multiple mutually contradictory accounts of what he in fact taught and what he did with the Tesla coil. In a recent report of an interview with Freshwater all those themes are repeated. It’s of note that the interview is on a web site with the motto “Restoring Truth to History Class,” one of whose recent emphases appears to be on Islamic infiltration into public school curricula in the U.S.

Given the false statements in its Freshwater story, I wonder what “truth” means to that site. The first paragraph of the story has four sentences. Every sentence has an error of fact. Below the fold I’ll walk through parts of the story, pointing out some of the distortions, misrepresentations, and plain falsehoods it contains.

Jerry Coyne has just gotten many of his oft-repeated New Atheist talking points published in the premier journal Evolution. You can read it here (blog here). On a first skim through the article – all I can manage in the near future, I’m afraid – here are a few points which are problematic for Coyne’s position, which I would have liked to see him address:

It has been announced that Robert Sokal died on April 9. I wrote a brief obituary here last autumn for his co-worker Peter Sneath. Together they pioneered the use of clustering algorithms in taxonomy, and argued for the adoption of phenetic methods based on clustering there. While they were ultimately unsuccessful in this, they became founding fathers of work on mathematical clustering, and their book Principles of Numerical Taxonomy was widely-noticed and greatly stimulated the development of phylogeny algorithms. A paper by Michener and Sokal (1957) is, as far as I can tell, the first one publishing a numerical phylogeny. His publication of the 1965 paper by Camin and Sokal in Evolution, and a visit he made to the University of Chicago that year, inspired me to start working on phylogeny algorithms.

Robert Sokal in 1964 at the International
Entomological Congress in London

Bob Sokal, more recently

Bob’s Stony Brook colleague Michael Bell has written a fine obituary, which I reprint below with his permission.

Williamstown, Kentucky, a city that is apparently near the fantasied location of the Ark Park (or is that the location of the fantasied Ark Park?) Is apparently letting that fantasy go to its corporate head, according to this article. The funniest line in the article? I am glad you asked:

The plans are based on the needs of the city and not the needs of the Ark Encounter, said [spokesman for the Kentucky League of Cities Tad] Long.

Inspired (I think) by that article, reader Dan Phelps sent us the following proposal to develop a coastline to spur economic development in Kentucky.

Recall that John Freshwater, former middle school science teacher in the Mt. Vernon (Ohio) City Schools, appealed his termination to the Knox County Court of Common Pleas, which denied his appeal. He then appealed to the Ohio 5th District Court of Appeals, which also denied the appeal. Now he is appealing to the Ohio Supreme Court. Today he filed a Memorandum in Support of Jurisdiction (MIS) with that court. The MIS is filed by R. Kelly Hamilton, Freshwater’s personal attorney, who is identified as “Affiliate Attorney with The Rutherford Institute”. The appeal document is up on NCSE’s site.

I have not done a detailed comparison of Freshwater’s (really, Rutherford’s) appeals court brief with the Supreme Court appeal, but a fast reading suggests they make essentially the same arguments.

In the Supreme Court document, which is essentially a condensed version (14 vs. 33 pages) of the brief submitted to the Ohio 5th District Court of Appeals, Freshwater once again makes the academic freedom and free speech arguments that were raised in his 5th District brief, as well as raising the “religious hostility” argument he made in that appeal. Both documents refer to “competing academic theories,” echoing the appeals brief’s claim that Freshwater only taught “alternative theories,” never mentioning the intelligent design and creationist materials he used. His behavior in that regard is called “neutrality toward religion.” The MIS says that

The fact that one competing theory on the formation of the universe and the beginning of life is consistent with the teachings of multiple major world religions simply does not justify interference with students’ and teachers’ academic freedom.

…

Additionally, the Board’s action manifests a clear and distinct hostility toward the major world religions whose teachings are consistent with the alternative theories discussed in Freshwater’s classes. (pp. 5-6)

As with the appeals court brief, the appeal to the Supreme Court does not actually get around to mentioning just what “alternative theories” Freshwater taught. In sworn testimony in the administrative hearing Freshwater denied teaching creationism. In an interview with faux-historian David Barton, Freshwater claimed to have taught “robust” evolution, teaching the evidence for and against. Now he says he taught “alternative theories.” One wonders what they were. Lysenkoism? Lamarckism? Mutationism? What?

The appeal claims that “Moreover, the academic freedom concern expressed here is of heightened importance because it involves the banishment of academic theories from the classroom based solely on the fact that they are consistent with certain religious traditions.” That is the core of the Rutherford Institute’s approach in this case, and represents an instance of the broader ID strategy to reverse the causal arrow between creationism and religion. It seeks to make the former the prime mover, not the latter. By very carefully not naming the “alternative theories” Freshwater supposedly taught, the Rutherford Institute is once again trying to slide creationism into public school curricula without actually naming it. It’s just coincidence that religion-based creationism is consistent with those alternative academic theories. Nothing to see here, folks. Move along.

Now that the bill has passed (although the governor decided not to sign it, a small (very small) victory for all the science and education organizations that opposed the bill), Wood has put up another post both (a) explaining what happened to the letter and (b) explaining in much more detail the problems with the law and with the whole misbegotten creationist/ID strategy of trying to get their stuff into the schools through political means rather than the responsible way of convincing the scientific community.

1. Wood says he took the letter down of his own free will. He said, “I can make my own decisions to take down a blog post that in retrospect doesn’t meet my own quality standards.” Confusingly, though, Wood didn’t say what was lacking in the letter. Wood certainly didn’t change his position on the bill, which if anything more negative and less diplomatic now than it was then.

2. Although Wood claims no one turned the screws on him, I think it is pretty clear that the creationist lobby tried. This is Wood’s summary of what one of his friends told him:

I know that law is not my expertise, so when I get a letter from a trusted friend saying that my opinion is “legally and politically naive” I listen.

Actually, Wood’s letter was legally and politically canny in many ways. The only way it was naive was in the statements that the law was unnecessary for creationists and that it would have no effect on education, but presumably that was not the naivet� that Wood’s presumably creationist friend was talking about. The law is necessary if you want to increase the teaching of creationist/IDist B.S. in Tennessee public schools.

Then, even more incredibly, Wood reports that John West of the Discovery Institute – yes, the Discovery “we’re not creationists, especially not young-earth-just-fell-off-the-turnip-truck creationists” Institute – apparently circulated a letter to Bryan College employees lambasting Wood for daring to be a creationist with an independent voice who doesn’t think creationism should be pushed in the political arena before it succeeds in the scientific arena:

Back to my own experience: I took my letter to the governor down less than 24 hours after I put it up, and a few days later, a staff member at the college passed along a letter from John West of the Discovery Institute trying to drum up some resistance on the Bryan campus to my opinion. As far as I know, his efforts had zero effect on campus, since I didn’t hear from any other person on campus about it. In his letter, West described me as “one cranky self-described ‘creationist’ who seems to get his facts from Panda’s Thumb.”

I guess Todd Wood, young-earther and professor at William Jennings Bryan College, isn’t creationist enough for the Discovery Institute’s John West! And that’s quite something.

I suppose that I should mention that I had absolutely no direct information, apart from the removal of Wood’s open letter, that the Discovery Institute’s screw-turning shenanigans were going on when I wrote:

Did someone at Bryan College object to a creationist going off-message? Did someone at the Discovery Institute get worried about the influence that a Tennessee-based professional creationist opposing the law would have, and call up Bryan College or Wood himself and start harassing them?

According to Wood, this sort of thing wasn’t the cause of him taking down the letter – but nevertheless exactly these sorts of attempts were actually made! Am I psychic, or do I just know how these guys operate? We report, you decide.

Discussion of creationism in public school classrooms in Tennessee will now be permitted under a bill that passed the Republican-controlled state Legislature despite opposition from the state’s Republican governor.

The measure will allow classroom debates over evolution, permitting discussions of creationism alongside evolutionary teachings about the origins of life. Critics say the law, disparagingly called “The Monkey Bill,” will plunge Tennessee back to the divisive days of the notorious Scopes “Monkey Trial” in Dayton, Tenn., in 1925.

Gov. Bill Haslam refused Tuesday to sign the bill, saying it would create confusion over schools’ science curriculum. But the bill became law anyway. Haslam said he decided not to use his veto power, because the Legislature had the votes to override a veto. The measure passed by a 3-to-1 margin.

“Good legislation should bring clarity and not confusion,” Haslam said, according to Reuters. “My concern is that this bill has not met this objective.”

The state’s teachers are not allowed to raise alternatives to evolution but, under the new law, would be required to permit discussion of creationism and other beliefs if they are raised in class. The law would also permit discussion of challenges to such scientific conclusions as the man-made effects of climate change.

Any guesses as to how long before this gets litigious?

I wrote Gov. Haslam last week, noting that comedians like Jay Leno and David Letterman would soon be mocking Tennessee if the bill wasn’t vetoed. If anyone knows of mentions of the bill on comedy shows, post them here!

The distinguished philosopher Philip Kitcher has posted an opinion piece on social Darwinism in today’s New York Times. Carefully distinguishing social Darwinism from (its somewhat distant relatives) eugenics and racism, Kitcher notes that

The heart of social Darwinism is a pair of theses: first, people have intrinsic abilities and talents (and, correspondingly, intrinsic weaknesses), which will be expressed in their actions and achievements, independently of the social, economic and cultural environments in which they develop; second, intensifying competition enables the most talented to develop their potential to the full, and thereby to provide resources for a society that make life better for all.

Sphaerodactylus samanensis – adult male Haitises banded gecko. This is a sexually dimorphic species, with females and juveniles being black and white banded and lacking the yellow-orange head (remnants of this male’s juvenile pattern are still visible). This species is known only from the karst formations of the Los Haitises region of the Dominican Republic. This male is the furthest west this species has ever been found; unfortunately, there are serious plans to develop a cement factory just a few miles away.

Correction: See this comment and this one. Operating from memory, I mis-stated Behe’s argument below. According to Behe’s “CCC” criterion, chloroquine resistance is (barely) within the capabilities of evolution given the time and population size available. It’s the “double CCC” that’s unevolvable according to Behe. Malaria itself, however, was designed according to Behe, and the case of artemesinin resistance is still open.

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In “The Edge of Evolution”(reviewed here and here), Michael Behe argued explicitly that an intelligent agent is responsible for the evolution of chloroquine-resistant malaria, arguing that the necessary mutations are beyond the reach of chance and selection given the time and population sizes available. Therefore, he claimed, an intelligent designer is responsible for drug-resistant malaria. He wrote

Here’s something to ponder long and hard: Malaria was intentionally designed. The molecular machinery with which the parasite invades red blood cells is an exquisitely purposeful arrangement of parts. C-Eve’s children died in her arms partly because an intelligent agent deliberately made malaria, or at least something very similar to it. (p. 237)

Not only that, the purported intelligent agent is responsible for drug resistance in malaria. Behe claimed that because it requires multiple independent mutations, none adaptive by themselves, given the time and population sizes available malarial resistance to chloroquine must have been designed (and presumably manufactured) by an intelligent agent (see his Chapter 3 for elaborate probability calculations). And chloroquine resistance in malaria is now nearly universal.

The currently most effective first-choice treatment for otherwise drug-resistant malaria is artemisinin. Hailed in 2004 as a “magic bullet” against malaria, artemisinin is an extract of a plant grown mainly in Viet Nam. Just a few years later, an artemisinin-resistant strain of malaria appeared in southeast Asia. In fact, according to this paper in Science published yesterday, April 6, 2012, 33 regions on the falciparum malaria genome appear to be under strong selection for artemisinin resistance. (See a news story here.) 33 genome regions on chromosome 13 that are under selection for artemisinin resistance! Surely in Behe’s fantasy world that’s way beyond the capabilities of evolution, and his malevolent intelligent agent is working over-time in Cambodia and Thailand to kill people.

Behe also discussed the research of Barry Hall on a class of antibiotic drugs called carbapenems. He approvingly quoted Hall as writing

“The results predict, with 99.9% confidence, that even under intense selection the [enzyme] will not evolve to confer increased resistance to imipenem [a member of the carbapenems].” (p. 237)

Behe continued, in his own words,

In other words, more than two evolutionary steps would have to be skipped to achieve resistance, effectively ruling out Darwinian evolution. (p. 237).

So if resistance to carbapenems (of which imipenem is an instance) should appear, according to Behe it must have been due to an intelligent agent. But even before Behe published that (“Edge of Evolution” was published in 2007), carbamenem-resistant gram negative bacteria were being detected in 2005. Again, in Behe’s fantasy world, a malevolent intelligent agent is hard at work right now, designing (and manufacturing) pathogens to kill people.

This month’s theme is: the Tree (structures) of Life. Since this blog covers a mix of both biological and computational content, it is fitting that we explore this month’s submissions in the context of trees (the computational kind) and biological classification (the biological kind). I will indulge in a historical and technical overview of trees used in evolutionary analysis, then present this month’s posts.

Cyclopean here means one-eyed (note the lens on the left flange). Never mind that the dictionary thinks it means gigantic; we have plenty of synonyms for gigantic. The antenna responds to centimeter waves and is tuned to detect pheromones. The waveguide has only one internal organ, which serves as both mouth and rectum; it is especially well adapted to politics.